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      Biochemical and structural characterization of a thermostable Dps protein with His‐type ferroxidase centers and outer metal‐binding sites

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          Abstract

          The DNA‐binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 ( TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.

          Abstract

          A DNA‐binding protein from starved cells (Dps) protein from nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 ( TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 illustrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein.

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          Most cited references29

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          Bacterial iron homeostasis.

          Iron is essential to virtually all organisms, but poses problems of toxicity and poor solubility. Bacteria have evolved various mechanisms to counter the problems imposed by their iron dependence, allowing them to achieve effective iron homeostasis under a range of iron regimes. Highly efficient iron acquisition systems are used to scavenge iron from the environment under iron-restricted conditions. In many cases, this involves the secretion and internalisation of extracellular ferric chelators called siderophores. Ferrous iron can also be directly imported by the G protein-like transporter, FeoB. For pathogens, host-iron complexes (transferrin, lactoferrin, haem, haemoglobin) are directly used as iron sources. Bacterial iron storage proteins (ferritin, bacterioferritin) provide intracellular iron reserves for use when external supplies are restricted, and iron detoxification proteins (Dps) are employed to protect the chromosome from iron-induced free radical damage. There is evidence that bacteria control their iron requirements in response to iron availability by down-regulating the expression of iron proteins during iron-restricted growth. And finally, the expression of the iron homeostatic machinery is subject to iron-dependent global control ensuring that iron acquisition, storage and consumption are geared to iron availability and that intracellular levels of free iron do not reach toxic levels.
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            A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli.

            A starvation-inducible DNA-binding protein was discovered as a result of the analysis of proteins synthesized in 3-day-old cultures of Escherichia coli. This 19-kD protein, designated Dps, is abundant in starved cells. In vitro, Dps forms extremely stable complexes with DNA, without apparent sequence specificity. When complexed with Dps, DNA is rendered DNase resistant. Mutant cells lacking Dps show dramatic changes in the pattern of proteins synthesized during starvation. The mutants also fail to develop starvation-induced resistance to hydrogen peroxide, an agent that can cause oxidative damage to DNA in vivo. These results have prompted us to postulate that Dps plays an important role both in gene expression and DNA protection during stationary phase. The existence of similar proteins, heretofore with no known function, in bacterial species distantly related to Escherichia coli suggests that Dps may define a novel class of widely conserved DNA-binding proteins.
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              KAMO : towards automated data processing for microcrystals

              An automated data-processing pipeline for protein microcrystals is presented. The processing of multiple small-wedge data sets was made dramatically easier by this pipeline.
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                Author and article information

                Contributors
                minato.takuo.219@m.kyushu-u.ac.jp
                yoon@i2cner.kyushu-u.ac.jp
                Journal
                FEBS Open Bio
                FEBS Open Bio
                10.1002/(ISSN)2211-5463
                FEB4
                FEBS Open Bio
                John Wiley and Sons Inc. (Hoboken )
                2211-5463
                28 May 2020
                July 2020
                : 10
                : 7 ( doiID: 10.1002/feb4.v10.7 )
                : 1219-1229
                Affiliations
                [ 1 ] Department of Chemistry and Biochemistry Graduate School of Engineering Kyushu University Fukuoka Japan
                [ 2 ] International Institute for Carbon‐Neutral Energy Research (WPI‐I2CNER) Kyushu University Fukuoka Japan
                [ 3 ] Department of Bioscience and Biotechnology Faculty of Agriculture Kyushu University Fukuoka Japan
                [ 4 ] Laboratory of Structural Biology Graduate School of System Life Sciences Kyushu University Fukuoka Japan
                [ 5 ] Center for Small Molecule Energy Kyushu University Fukuoka Japan
                Author notes
                [*] [* ] Correspondence

                T. Minato and K. ‐S. Yoon, Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto‐oka, Nishi‐ku, Fukuoka 819‐0395, Japan

                Tel: +81‐92‐802‐6688

                E‐mails: minato.takuo.219@ 123456m.kyushu-u.ac.jp (TM); yoon@ 123456i2cner.kyushu-u.ac.jp (KY)

                Author information
                https://orcid.org/0000-0002-4372-2906
                Article
                FEB412837
                10.1002/2211-5463.12837
                7327923
                32170832
                37cdac01-d8a9-4da9-a877-540505ee3945
                © 2020 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 January 2020
                : 06 March 2020
                : 11 March 2020
                Page count
                Figures: 5, Tables: 0, Pages: 11, Words: 6505
                Funding
                Funded by: Core Research for Evolutional Science and Technology , open-funder-registry 10.13039/501100003382;
                Award ID: JPMJCR18R2
                Funded by: Japan Society for the Promotion of Science , open-funder-registry 10.13039/501100001691;
                Award ID: 18H02091
                Award ID: 18J00191
                Funded by: World Premier International Research Center Initiative (WPI), Japan
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                July 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.5 mode:remove_FC converted:01.07.2020

                cyanobacteria,dna‐binding protein from starved cells,his‐type ferroxidase center,metal‐binding site,thermostability

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